Origin IGS: ttgtttctcctgtctgtgatttttttgtaaaaatccttcaattctttctatgcgttaatagataacagctttcttaaaaaaatctccctcgcttaaagtttcctttaaggtttctttaagctttttaagttaggctagtacatggaaaatttaccaatagaaccaaacttaatgttttaagttagatgctttgagcagtatctccatttgataaacctagtaaacagtccttaaaccaatcctaggattgacaagggcgttttagatttgtcaaaaggggcgcaaaaaagcagatgccaaaaacatttgttcttgcgttcttaaatactatacaaagcaagttctcttgcaaaatttctcatgcttttagatgcaggttaaaccgtgtgtgtgtgaagttggtttaacccgaatcatcaagcagccagtgccataagataagaattcttgtcttatggttttttctttttaccgatatgcatattttggtaggaaatgctaggaacaaaagctttatttgctttaaaaaacatttacctatcacagtatatgacataattgacatcttgtcaacaggtttgcctcgaaaaaaatgattgcatttaaaaaaatgtttaattttgataaaaccttgttatatcaagctttttgacacttttttaaagcgtttttttacttcgaggataaaaaaacagcaaatttttttgaggaaatttcccctttactgcttctttttcaaccttcagatggacagtgtgacagcatctgtcctcttctaatcggtagtcgatatgcttaggaaaggcgcttcaggacaaggcttagcaagctttgcctgtttcttcctacccaatagtatatgctaaagaaaatgcattgtcaatacatttgcattttattatatgtaaaacctatctaaaaatgcacaatgtactcagcttgtctattttttatagaaaaactacaaaatcaaaaaggctagaattttcagacaaaactacattgttatattataatagaagaaagaactccagaaaataatatttcctggagttcttttaatatgctacaaacttataagattacaacttgagcccttgatacctttgaaatagtatcttcttattatacaccaaaagactgagataatttcatggctggtctaaagtttatattaagatagtagatgtttttcaaatcaataaac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtttattgatttgaaaaacatctactatcttaatataaactttagaccagccatgaaattatctcagtcttttggtgtataataagaagatactatttcaaaggtatcaagggctcaagttgtaatcttataagtttgtagcatattaaaagaactccaggaaatattattttctggagttctttcttctattataatataacaatgtagttttgtctgaaaattctagcctttttgattttgtagtttttctataaaaaatagacaagctgagtacattgtgcatttttagataggttttacatataataaaatgcaaatgtattgacaatgcattttctttagcatatactattgggtaggaagaaacaggcaaagcttgctaagccttgtcctgaagcgcctttcctaagcatatcgactaccgattagaagaggacagatgctgtcacactgtccatctgaaggttgaaaaagaagcagtaaaggggaaatttcctcaaaaaaatttgctgtttttttatcctcgaagtaaaaaaacgctttaaaaaagtgtcaaaaagcttgatataacaaggttttatcaaaattaaacatttttttaaatgcaatcatttttttcgaggcaaacctgttgacaagatgtcaattatgtcatatactgtgataggtaaatgttttttaaagcaaataaagcttttgttcctagcatttcctaccaaaatatgcatatcggtaaaaagaaaaaaccataagacaagaattcttatcttatggcactggctgcttgatgattcgggttaaaccaacttcacacacacacggtttaacctgcatctaaaagcatgagaaattttgcaagagaacttgctttgtatagtatttaagaacgcaagaacaaatgtttttggcatctgcttttttgcgccccttttgacaaatctaaaacgcccttgtcaatcctaggattggtttaaggactgtttactaggtttatcaaatggagatactgctcaaagcatctaacttaaaacattaagtttggttctattggtaaattttccatgtactagcctaacttaaaaagcttaaagaaaccttaaaggaaactttaagcgagggagatttttttaagaaagctgttatctattaacgcatagaaagaattgaaggatttttacaaaaaaatcacagacaggagaaacaa Mask Tandem Repeat Region ================================================ ttgtttctcctgtctgtgatttttttgtaaaaatccttcaattctttctatgcgttaatagataacagctttcttaaaaaaatctccctcgcttaaagtttcctttaaggtttctttaagctttttaagttaggctagtacatggaaaatttaccaatagaaccaaacttaatgttttaagttagatgctttgagcagtatctccatttgataaacctagtaaacagtccttaaaccaatcctaggattgacaagggcgttttagatttgtcaaaaggggcgcaaaaaagcagatgccaaaaacatttgttcttgcgttcttaaatactatacaaagcaagttctcttgcaaaatttctcatgcttttagatgcaggttaaaccgtgtgtgtgtgaagttggtttaacccgaatcatcaagcagccagtgccataagataagaattcttgtcttatggttttttctttttaccgatatgcatattttggtaggaaatgctaggaacaaaagctttatttgctttaaaaaacatttacctatcacagtatatgacataattgacatcttgtcaacaggtttgcctcgaaaaaaatgattgcatttaaaaaaatgtttaattttgataaaaccttgttatatcaagctttttgacacttttttaaagcgtttttttacttcgaggataaaaaaacagcaaatttttttgaggaaatttcccctttactgcttctttttcaaccttcagatggacagtgtgacagcatctgtcctcttctaatcggtagtcgatatgcttaggaaaggcgcttcaggacaaggcttagcaagctttgcctgtttcttcctacccaatagtatatgctaaagaaaatgcattgtcaatacatttgcattttattatatgtaaaacctatctaaaaatgcacaatgtactcagcttgtctattttttatagaaaaactacaaaatcaaaaaggctagaattttcagacaaaactacattgttatattataatagaagaaagaactccagaaaataatatttcctggagttcttttaatatgctacaaacttataagattacaacttgagcccttgatacctttgaaatagtatcttcttattatacaccaaaagactgagataatttcatggctggtctaaagtttatattaagatagtagatgtttttcaaatcaataaac Find is-nt database================================================ Query_seq: SSA_2318:SSA_2320|SSA_2318:SSA_2320:PilB-like pili biogenesis ATPase, putative:hypothetical protein:<-<-:2321185..2322391 1207 ttgtttctcctgtctgtgatttttttgtaaaaatccttcaattctttctatgcgttaatagataacagctttcttaaaaaaatctccctcgcttaaagtttcctttaaggtttctttaagctttttaagttaggctagtacatggaaaatttaccaatagaaccaaacttaatgttttaagttagatgctttgagcagtatctccatttgataaacctagtaaacagtccttaaaccaatcctaggattgacaagggcgttttagatttgtcaaaaggggcgcaaaaaagcagatgccaaaaacatttgttcttgcgttcttaaatactatacaaagcaagttctcttgcaaaatttctcatgcttttagatgcaggttaaaccgtgtgtgtgtgaagttggtttaacccgaatcatcaagcagccagtgccataagataagaattcttgtcttatggttttttctttttaccgatatgcatattttggtaggaaatgctaggaacaaaagctttatttgctttaaaaaacatttacctatcacagtatatgacataattgacatcttgtcaacaggtttgcctcgaaaaaaatgattgcatttaaaaaaatgtttaattttgataaaaccttgttatatcaagctttttgacacttttttaaagcgtttttttacttcgaggataaaaaaacagcaaatttttttgaggaaatttcccctttactgcttctttttcaaccttcagatggacagtgtgacagcatctgtcctcttctaatcggtagtcgatatgcttaggaaaggcgcttcaggacaaggcttagcaagctttgcctgtttcttcctacccaatagtatatgctaaagaaaatgcattgtcaatacatttgcattttattatatgtaaaacctatctaaaaatgcacaatgtactcagcttgtctattttttatagaaaaactacaaaatcaaaaaggctagaattttcagacaaaactacattgttatattataatagaagaaagaactccagaaaataatatttcctggagttcttttaatatgctacaaacttataagattacaacttgagcccttgatacctttgaaatagtatcttcttattatacaccaaaagactgagataatttcatggctggtctaaagtttatattaagatagtagatgtttttcaaatcaataaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2318:SSA_2320|SSA_2318:SSA_2320:PilB-like pili biogenesis ATPase, putative:hypothetical protein:<-<-:2321185..2322391 1207 ttgtttctcctgtctgtgatttttttgtaaaaatccttcaattctttctatgcgttaatagataacagctttcttaaaaaaatctccctcgcttaaagtttcctttaaggtttctttaagctttttaagttaggctagtacatggaaaatttaccaatagaaccaaacttaatgttttaagttagatgctttgagcagtatctccatttgataaacctagtaaacagtccttaaaccaatcctaggattgacaagggcgttttagatttgtcaaaaggggcgcaaaaaagcagatgccaaaaacatttgttcttgcgttcttaaatactatacaaagcaagttctcttgcaaaatttctcatgcttttagatgcaggttaaaccgtgtgtgtgtgaagttggtttaacccgaatcatcaagcagccagtgccataagataagaattcttgtcttatggttttttctttttaccgatatgcatattttggtaggaaatgctaggaacaaaagctttatttgctttaaaaaacatttacctatcacagtatatgacataattgacatcttgtcaacaggtttgcctcgaaaaaaatgattgcatttaaaaaaatgtttaattttgataaaaccttgttatatcaagctttttgacacttttttaaagcgtttttttacttcgaggataaaaaaacagcaaatttttttgaggaaatttcccctttactgcttctttttcaaccttcagatggacagtgtgacagcatctgtcctcttctaatcggtagtcgatatgcttaggaaaggcgcttcaggacaaggcttagcaagctttgcctgtttcttcctacccaatagtatatgctaaagaaaatgcattgtcaatacatttgcattttattatatgtaaaacctatctaaaaatgcacaatgtactcagcttgtctattttttatagaaaaactacaaaatcaaaaaggctagaattttcagacaaaactacattgttatattataatagaagaaagaactccagaaaataatatttcctggagttcttttaatatgctacaaacttataagattacaacttgagcccttgatacctttgaaatagtatcttcttattatacaccaaaagactgagataatttcatggctggtctaaagtttatattaagatagtagatgtttttcaaatcaataaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2318:SSA_2320|SSA_2318:SSA_2320:PilB-like pili biogenesis ATPase, putative:hypothetical protein:<-<-:2321185..2322391 1207 ttgtttctcctgtctgtgatttttttgtaaaaatccttcaattctttctatgcgttaatagataacagctttcttaaaaaaatctccctcgcttaaagtttcctttaaggtttctttaagctttttaagttaggctagtacatggaaaatttaccaatagaaccaaacttaatgttttaagttagatgctttgagcagtatctccatttgataaacctagtaaacagtccttaaaccaatcctaggattgacaagggcgttttagatttgtcaaaaggggcgcaaaaaagcagatgccaaaaacatttgttcttgcgttcttaaatactatacaaagcaagttctcttgcaaaatttctcatgcttttagatgcaggttaaaccgtgtgtgtgtgaagttggtttaacccgaatcatcaagcagccagtgccataagataagaattcttgtcttatggttttttctttttaccgatatgcatattttggtaggaaatgctaggaacaaaagctttatttgctttaaaaaacatttacctatcacagtatatgacataattgacatcttgtcaacaggtttgcctcgaaaaaaatgattgcatttaaaaaaatgtttaattttgataaaaccttgttatatcaagctttttgacacttttttaaagcgtttttttacttcgaggataaaaaaacagcaaatttttttgaggaaatttcccctttactgcttctttttcaaccttcagatggacagtgtgacagcatctgtcctcttctaatcggtagtcgatatgcttaggaaaggcgcttcaggacaaggcttagcaagctttgcctgtttcttcctacccaatagtatatgctaaagaaaatgcattgtcaatacatttgcattttattatatgtaaaacctatctaaaaatgcacaatgtactcagcttgtctattttttatagaaaaactacaaaatcaaaaaggctagaattttcagacaaaactacattgttatattataatagaagaaagaactccagaaaataatatttcctggagttcttttaatatgctacaaacttataagattacaacttgagcccttgatacctttgaaatagtatcttcttattatacaccaaaagactgagataatttcatggctggtctaaagtttatattaagatagtagatgtttttcaaatcaataaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgtttctcctgtctgtgatttttttgtaaaaatccttcaattctttctatgcgttaatagataacagctttcttaaaaaaatctccctcgcttaaagtttcctttaaggtttctttaagctttttaagttaggctagtacatggaaaatttaccaatagaaccaaacttaatgttttaagttagatgctttgagcagtatctccatttgataaacctagtaaacagtccttaaaccaatcctaggattgacaagggcgttttagatttgtcaaaaggggcgcaaaaaagcagatgccaaaaacatttgttcttgcgttcttaaatactatacaaagcaagttctcttgcaaaatttctcatgcttttagatgcaggttaaaccgtgtgtgtgtgaagttggtttaacccgaatcatcaagcagccagtgccataagataagaattcttgtcttatggttttttctttttaccgatatgcatattttggtaggaaatgctaggaacaaaagctttatttgctttaaaaaacatttacctatcacagtatatgacataattgacatcttgtcaacaggtttgcctcgaaaaaaatgattgcatttaaaaaaatgtttaattttgataaaaccttgttatatcaagctttttgacacttttttaaagcgtttttttacttcgaggataaaaaaacagcaaatttttttgaggaaatttcccctttactgcttctttttcaaccttcagatggacagtgtgacagcatctgtcctcttctaatcggtagtcgatatgcttaggaaaggcgcttcaggacaaggcttagcaagctttgcctgtttcttcctacccaatagtatatgctaaagaaaatgcattgtcaatacatttgcattttattatatgtaaaacctatctaaaaatgcacaatgtactcagcttgtctattttttatagaaaaactacaaaatcaaaaaggctagaattttcagacaaaactacattgttatattataatagaagaaagaactccagaaaataatatttcctggagttcttttaatatgctacaaacttataagattacaacttgagcccttgatacctttgaaatagtatcttcttattatacaccaaaagactgagataatttcatggctggtctaaagtttatattaagatagtagatgtttttcaaatcaataaac Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 266 End: 367 ......................................................................................................................................................................................................................................................................... M C Q K G R K K A D A K N I C S C V L K Y Y T K Q V L L Q N F S C F ........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ Protein_Len: 37 Strand: + Start: 294 End: 404 ..................................................................................................................................................................................................................................................................................................... M P K T F V L A F L N T I Q S K F S C K I S H A F R C R L N R V C V K L V ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 52 Strand: + Start: 438 End: 593 ..................................................................................................................................................................................................................................................................................................................................................................................................................................................... M R I L V L W F F L F T D M H I L V G N A R N K S F I C F K K H L P I T V Y D I I D I L S T G L P R K K ...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 597 End: 776 .................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... M H L K K C L I L I K P C Y I K L F D T F L K R F F T S R I K K Q Q I F L R K F P L Y C F F F N L Q M D S V T A S V L F ............................................................................................................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 832 End: 1038 ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... M P V S S Y P I V Y A K E N A L S I H L H F I I C K T Y L K M H N V L S L S I F Y R K T T K S K R L E F S D K T T L L Y ......................................................................................................................................................................... Protein_Len: 43 Strand: - Start: 663 End: 791 ...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... L T K K S R P Y F F L L N K Q P F K G K V A E K E V K L H V T H C C R D E E L R Y D M ................................................................................................................................................................................................................................................................................................................................................................................................................................ Protein_Len: 60 Strand: - Start: 407 End: 625 ...................................................................................................................................................................................................................................................................................................................................................................................................................... R T K H N K R K V S I C I K T P F A L F L L K I Q K L F C K G I V T Y S M I S M K D V P K G R F F H N C K F F H K I K M ...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 37 Strand: - Start: 245 End: 355 .................................................................................................................................................................................................................................................... S Q C P R K L N T L L P A F F C I G F V N T R A N K F V I C L L N E Q L M .................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... ttgtttctcctgtctgtgatttttttgtaaaaatccttcaattctttctatgcgttaatagataacagctttcttaaaaaaatctccctcgcttaaagtttcctttaaggtttctttaagctttttaagttaggctagtacatggaaaatttaccaatagaaccaaacttaatgttttaagttagatgctttgagcagtatctccatttgataaacctagtaaacagtccttaaaccaatcctaggattgacaagggcgttttagatttgtcaaaaggggcgcaaaaaagcagatgccaaaaacatttgttcttgcgttcttaaatactatacaaagcaagttctcttgcaaaatttctcatgcttttagatgcaggttaaaccgtgtgtgtgtgaagttggtttaacccgaatcatcaagcagccagtgccataagataagaattcttgtcttatggttttttctttttaccgatatgcatattttggtaggaaatgctaggaacaaaagctttatttgctttaaaaaacatttacctatcacagtatatgacataattgacatcttgtcaacaggtttgcctcgaaaaaaatgattgcatttaaaaaaatgtttaattttgataaaaccttgttatatcaagctttttgacacttttttaaagcgtttttttacttcgaggataaaaaaacagcaaatttttttgaggaaatttcccctttactgcttctttttcaaccttcagatggacagtgtgacagcatctgtcctcttctaatcggtagtcgatatgcttaggaaaggcgcttcaggacaaggcttagcaagctttgcctgtttcttcctacccaatagtatatgctaaagaaaatgcattgtcaatacatttgcattttattatatgtaaaacctatctaaaaatgcacaatgtactcagcttgtctattttttatagaaaaactacaaaatcaaaaaggctagaattttcagacaaaactacattgttatattataatagaagaaagaactccagaaaataatatttcctggagttcttttaatatgctacaaacttataagattacaacttgagcccttgatacctttgaaatagtatcttcttattatacaccaaaagactgagataatttcatggctggtctaaagtttatattaagatagtagatgtttttcaaatcaataaac Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 89 Start: 855 End: 884 ......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ATTGACAATGCATTTTCTTTAGCATATACT................................................................................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 88 Start: 545 End: 574 ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTTGACAAGATGTCAATTATGTCATATACT......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 648 End: 677 .......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTTGACACTTTTTTAAAGCGTTTTTTTACT.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 1010 End: 1039 .................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ATTTTCTGGAGTTCTTTCTTCTATTATAAT........................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 1169 End: 1198 ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTTGAAAAACATCTACTATCTTAATATAAA......... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttgtttctcctgtctgtgatttttttgtaaaaatccttcaattctttctatgcgttaatagataacagctttcttaaaaaaatctccctcgcttaaagtttcctttaaggtttctttaagctttttaagttaggctagtacatggaaaatttaccaatagaaccaaacttaatgttttaagttagatgctttgagcagtatctccatttgataaacctagtaaacagtccttaaaccaatcctaggattgacaagggcgttttagatttgtcaaaaggggcgcaaaaaagcagatgccaaaaacatttgttcttgcgttcttaaatactatacaaagcaagttctcttgcaaaatttctcatgcttttagatgcaggttaaaccgtgtgtgtgtgaagttggtttaacccgaatcatcaagcagccagtgccataagataagaattcttgtcttatggttttttctttttaccgatatgcatattttggtaggaaatgctaggaacaaaagctttatttgctttaaaaaacatttacctatcacagtatatgacataattgacatcttgtcaacaggtttgcctcgaaaaaaatgattgcatttaaaaaaatgtttaattttgataaaaccttgttatatcaagctttttgacacttttttaaagcgtttttttacttcgaggataaaaaaacagcaaatttttttgaggaaatttcccctttactgcttctttttcaaccttcagatggacagtgtgacagcatctgtcctcttctaatcggtagtcgatatgcttaggaaaggcgcttcaggacaaggcttagcaagctttgcctgtttcttcctacccaatagtatatgctaaagaaaatgcattgtcaatacatttgcattttattatatgtaaaacctatctaaaaatgcacaatgtactcagcttgtctattttttatagaaaaactacaaaatcaaaaaggctagaattttcagacaaaactacattgttatattataatagaagaaagaactccagaaaataatatttcctggagttcttttaatatgctacaaacttataagattacaacttgagcccttgatacctttgaaatagtatcttcttattatacaccaaaagactgagataatttcatggctggtctaaagtttatattaagatagtagatgtttttcaaatcaataaac Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 74 HP_score: -5.4 Tail_Score: -4.74504 Start: 91 End: 121 Full_Region: AAAAAAATCTCCCTC GCTTAAAGTTTCCT TTA AGGTTTCTTTAAGC TTTTTAAGTTAGGCT ..........................................................................................GCTTAAAGTTTCCTTTAAGGTTTCTTTAAGC.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 71 HP_score: -6.7 Tail_Score: -4.15197 Start: 337 End: 350 Full_Region: agcatgagaaatttt gcaag agaa cttgc tttgtatagtattta ................................................................................................................................................................................................................................................................................................................................................gcaagagaacttgc......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -12.2 Tail_Score: -5.93252 Start: 431 End: 458 Full_Region: ATCAAGCAGCCAGTG CCATAAGATAAG AATT CTTGTCTTATGG TTTTTTCTTTTTACC ..............................................................................................................................................................................................................................................................................................................................................................................................................................................CCATAAGATAAGAATTCTTGTCTTATGG............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 70 HP_score: -7.2 Tail_Score: -3.58365 Start: 559 End: 573 Full_Region: ttcgaggcaaacctg ttgaca aga tgtcaa ttatgtcatatactg ..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ttgacaagatgtcaa.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 75 HP_score: -2.8 Tail_Score: -5.63103 Start: 653 End: 667 Full_Region: TATCAAGCTTTTTGA CACTTT TTT AAAGCG TTTTTTTACTTCGAG ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CACTTTTTTAAAGCG............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ TransTerm Strand: + Conf: 93 HP_score: -10.0 Tail_Score: -4.24342 Start: 811 End: 838 Full_Region: TTAGGAAAGGCGCTT CAGGACAAGGCTT AGC AAGCTTTGCCTG TTTCTTCCTACCCAA ..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CAGGACAAGGCTTAGCAAGCTTTGCCTG................................................................................................................................................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 100 HP_score: -16.4 Tail_Score: -4.49353 Start: 1026 End: 1056 Full_Region: tgtagcatattaaaa gaactccaggaaat att attttctggagttc tttcttctattataa .................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................gaactccaggaaatattattttctggagttc....................................................................................................................................................... Find igs database================================================ Query_seq: SSA_2318:SSA_2320|SSA_2318:SSA_2320:PilB-like pili biogenesis ATPase, putative:hypothetical protein:<-<-:2321185..2322391 1207 ttgtttctcctgtctgtgatttttttgtaaaaatccttcaattctttctatgcgttaatagataacagctttcttaaaaaaatctccctcgcttaaagtttcctttaaggtttctttaagctttttaagttaggctagtacatggaaaatttaccaatagaaccaaacttaatgttttaagttagatgctttgagcagtatctccatttgataaacctagtaaacagtccttaaaccaatcctaggattgacaagggcgttttagatttgtcaaaaggggcgcaaaaaagcagatgccaaaaacatttgttcttgcgttcttaaatactatacaaagcaagttctcttgcaaaatttctcatgcttttagatgcaggttaaaccgtgtgtgtgtgaagttggtttaacccgaatcatcaagcagccagtgccataagataagaattcttgtcttatggttttttctttttaccgatatgcatattttggtaggaaatgctaggaacaaaagctttatttgctttaaaaaacatttacctatcacagtatatgacataattgacatcttgtcaacaggtttgcctcgaaaaaaatgattgcatttaaaaaaatgtttaattttgataaaaccttgttatatcaagctttttgacacttttttaaagcgtttttttacttcgaggataaaaaaacagcaaatttttttgaggaaatttcccctttactgcttctttttcaaccttcagatggacagtgtgacagcatctgtcctcttctaatcggtagtcgatatgcttaggaaaggcgcttcaggacaaggcttagcaagctttgcctgtttcttcctacccaatagtatatgctaaagaaaatgcattgtcaatacatttgcattttattatatgtaaaacctatctaaaaatgcacaatgtactcagcttgtctattttttatagaaaaactacaaaatcaaaaaggctagaattttcagacaaaactacattgttatattataatagaagaaagaactccagaaaataatatttcctggagttcttttaatatgctacaaacttataagattacaacttgagcccttgatacctttgaaatagtatcttcttattatacaccaaaagactgagataatttcatggctggtctaaagtttatattaagatagtagatgtttttcaaatcaataaac Intra-Species Hit: Count: 1 Min: 1 Max: 1207 Len: 1207 Subject: NC_009009_SSA_2318_SSA_2320|PilB-like pili biogenesis ATPase, putative:hypothetical protein|NEGATIVE:NEGATIVE|[2321185,2322391]|1207 HSP 1 e-value: 0.0 bit: 1041.0 Len: 645 Query Start:1 Query End:645 Subject Strand: POSITIVE Subject Start: 1 Subject End: 645 ttgtttctcctgtctgtgannnnnnngtaaaaatccttcaattctttctatgcgttaatagataacagctttcttnnnnnnntctccctcgcttaaagtttcctttaaggtttctttaagctttttaagttaggctagtacatggaaaatttaccaatagaaccaaacttaatgttttaagttagatgctttgagcagtatctccatttgataaacctagtaaacagtccttaaaccaatcctaggattgacaagggcgttttagatttgtcaaaaggggcgcaaaaaagcagatgccaaaaacatttgttcttgcgttcttaaatactatacaaagcaagttctcttgcaaaatttctcatgcttttagatgcaggttaaaccgtgtgtgtgtgaagttggtttaacccgaatcatcaagcagccagtgccataagataagaattcttgtcttatggnnnnnnnnnnnnaccgatatgcatattttggtaggaaatgctaggaacaaaagctttatttgctttaaaaaacatttacctatcacagtatatgacataattgacatcttgtcaacaggtttgcctcgnnnnnnntgattgcatttnnnnnnntgtttaattttgataaaaccttgttatatcaagc.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. ttgtttctcctgtctgtgatttttttgtaaaaatccttcaattctttctatgcgttaatagataacagctttcttaaaaaaatctccctcgcttaaagtttcctttaaggtttctttaagctttttaagttaggctagtacatggaaaatttaccaatagaaccaaacttaatgttttaagttagatgctttgagcagtatctccatttgataaacctagtaaacagtccttaaaccaatcctaggattgacaagggcgttttagatttgtcaaaaggggcgcaaaaaagcagatgccaaaaacatttgttcttgcgttcttaaatactatacaaagcaagttctcttgcaaaatttctcatgcttttagatgcaggttaaaccgtgtgtgtgtgaagttggtttaacccgaatcatcaagcagccagtgccataagataagaattcttgtcttatggttttttctttttaccgatatgcatattttggtaggaaatgctaggaacaaaagctttatttgctttaaaaaacatttacctatcacagtatatgacataattgacatcttgtcaacaggtttgcctcgaaaaaaatgattgcatttaaaaaaatgtttaattttgataaaaccttgttatatcaagc.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. HSP 2 e-value: 0.0 bit: 993.0 Len: 501 Query Start:707 Query End:1207 Subject Strand: POSITIVE Subject Start: 707 Subject End: 1207 ..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................gaggaaatttcccctttactgcttctttttcaaccttcagatggacagtgtgacagcatctgtcctcttctaatcggtagtcgatatgcttaggaaaggcgcttcaggacaaggcttagcaagctttgcctgtttcttcctacccaatagtatatgctaaagaaaatgcattgtcaatacatttgcattttattatatgtaaaacctatctaaaaatgcacaatgtactcagcttgtctattttttatagaaaaactacaaaatcaaaaaggctagaattttcagacaaaactacattgttatattataatagaagaaagaactccagaaaataatatttcctggagttcttttaatatgctacaaacttataagattacaacttgagcccttgatacctttgaaatagtatcttcttattatacaccaaaagactgagataatttcatggctggtctaaagtttatattaagatagtagatgtttttcaaatcaataaac ..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................gaggaaatttcccctttactgcttctttttcaaccttcagatggacagtgtgacagcatctgtcctcttctaatcggtagtcgatatgcttaggaaaggcgcttcaggacaaggcttagcaagctttgcctgtttcttcctacccaatagtatatgctaaagaaaatgcattgtcaatacatttgcattttattatatgtaaaacctatctaaaaatgcacaatgtactcagcttgtctattttttatagaaaaactacaaaatcaaaaaggctagaattttcagacaaaactacattgttatattataatagaagaaagaactccagaaaataatatttcctggagttcttttaatatgctacaaacttataagattacaacttgagcccttgatacctttgaaatagtatcttcttattatacaccaaaagactgagataatttcatggctggtctaaagtttatattaagatagtagatgtttttcaaatcaataaac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUUUCUCCUGUCUGUGAUUUUUUUGUAAAAAUCCUUCAAUUCUUUCUAUGCGUUAAUAGAUAACAGCUUUCUUAAAAAAAUCUCCCUCGCUUAAAGUUUCCUUUAAGGUUUCUUUAAGCUUUUUAAGUUAGGCUAGUACAUGGAAAAUUUACCAAUAGAACCAAACUUAAUGUUUUAAGUUAGAUGCUUUGAGCAGUAUCUCCAUUUGAUAAACCUAGUAAACAGUCCUUAAACCAAUCCUAGGAUUGACAAGGGCGUUUUAGAUUUGUCAAAAGGGGCGCAAAAAAGCAGAUGCCAAAAACAUUUGUUCUUGCGUUCUUAAAUACUAUACAAAGCAAGUUCUCUUGCAAAAUUUCUCAUGCUUUUAGAUGCAGGUUAAACCGUGUGUGUGUGAAGUUGGUUUAACCCGAAUCAUCAAGCAGCCAGUGCCAUAAGAUAAGAAUUCUUGUCUUAUGGUUUUUUCUUUUUACCGAUAUGCAUAUUUUGGUAGGAAAUGCUAGGAACAAAAGCUUUAUUUGCUUUAAAAAACAUUUACCUAUCACAGUAUAUGACAUAAUUGACAUCUUGUCAACAGGUUUGCCUCGAAAAAAAUGAUUGCAUUUAAAAAAAUGUUUAAUUUUGAUAAAACCUUGUUAUAUCAAGCUUUUUGACACUUUUUUAAAGCGUUUUUUUACUUCGAGGAUAAAAAAACAGCAAAUUUUUUUGAGGAAAUUUCCCCUUUACUGCUUCUUUUUCAACCUUCAGAUGGACAGUGUGACAGCAUCUGUCCUCUUCUAAUCGGUAGUCGAUAUGCUUAGGAAAGGCGCUUCAGGACAAGGCUUAGCAAGCUUUGCCUGUUUCUUCCUACCCAAUAGUAUAUGCUAAAGAAAAUGCAUUGUCAAUACAUUUGCAUUUUAUUAUAUGUAAAACCUAUCUAAAAAUGCACAAUGUACUCAGCUUGUCUAUUUUUUAUAGAAAAACUACAAAAUCAAAAAGGCUAGAAUUUUCAGACAAAACUACAUUGUUAUAUUAUAAUAGAAGAAAGAACUCCAGAAAAUAAUAUUUCCUGGAGUUCUUUUAAUAUGCUACAAACUUAUAAGAUUACAACUUGAGCCCUUGAUACCUUUGAAAUAGUAUCUUCUUAUUAUACACCAAAAGACUGAGAUAAUUUCAUGGCUGGUCUAAAGUUUAUAUUAAGAUAGUAGAUGUUUUUCAAAUCAAUAAAC .....(((.(((((((((.((((((((((((((.......((((......((((((..........(((((.((((((((..........((((((((...((.....))...))))))))))))))))..)))))....((((..((((((..(((.(((((..(((((((....)))))))...(((((((...(((((.....(((((((((.(((..((((.((((((....(((((....)))))..))))))))))))).)))))))))((((((((((...((((((((.......)))))))).))))))))))..)))))...))))))).))))).)))..))))))..))))......))))))((((((((((..............)))))))))).))))...(((((.(.(((((((((((((((((....)))))))))))...((((((((......((((((.((((..((((((((..(((.......(((((.......)))))............((((....((((((((((....(((((.....)))))..((....(((((((((((....((((.(((((((((.((((.((.(((((((.(((...))).))))))).))...)))).)))))))))..(((((((((((....)).))))))))).)))).)))))))))))......))....................(((...(((.(((((((((....))).))))))...)))....))).))).)))))))))))...)))....((((.(((((((.....)))))))))))....)))))))).))))))))))...)))))))).)))))).)..((((((((((((((...(((.(.....).)))...)))))))).))))))....))))).....)))))))))))))).)))...........((((((((.((((((....(((......)))....(((((((((((.(((((((((((.((((...)))).))))))))))).....((((((((((..((((((.(((.....)))...))).)))..))))...)))))))))).)))))))..........))))))....))).)))))..................)))))).))).................... (-311.84) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUAUUGAUUUGAAAAACAUCUACUAUCUUAAUAUAAACUUUAGACCAGCCAUGAAAUUAUCUCAGUCUUUUGGUGUAUAAUAAGAAGAUACUAUUUCAAAGGUAUCAAGGGCUCAAGUUGUAAUCUUAUAAGUUUGUAGCAUAUUAAAAGAACUCCAGGAAAUAUUAUUUUCUGGAGUUCUUUCUUCUAUUAUAAUAUAACAAUGUAGUUUUGUCUGAAAAUUCUAGCCUUUUUGAUUUUGUAGUUUUUCUAUAAAAAAUAGACAAGCUGAGUACAUUGUGCAUUUUUAGAUAGGUUUUACAUAUAAUAAAAUGCAAAUGUAUUGACAAUGCAUUUUCUUUAGCAUAUACUAUUGGGUAGGAAGAAACAGGCAAAGCUUGCUAAGCCUUGUCCUGAAGCGCCUUUCCUAAGCAUAUCGACUACCGAUUAGAAGAGGACAGAUGCUGUCACACUGUCCAUCUGAAGGUUGAAAAAGAAGCAGUAAAGGGGAAAUUUCCUCAAAAAAAUUUGCUGUUUUUUUAUCCUCGAAGUAAAAAAACGCUUUAAAAAAGUGUCAAAAAGCUUGAUAUAACAAGGUUUUAUCAAAAUUAAACAUUUUUUUAAAUGCAAUCAUUUUUUUCGAGGCAAACCUGUUGACAAGAUGUCAAUUAUGUCAUAUACUGUGAUAGGUAAAUGUUUUUUAAAGCAAAUAAAGCUUUUGUUCCUAGCAUUUCCUACCAAAAUAUGCAUAUCGGUAAAAAGAAAAAACCAUAAGACAAGAAUUCUUAUCUUAUGGCACUGGCUGCUUGAUGAUUCGGGUUAAACCAACUUCACACACACACGGUUUAACCUGCAUCUAAAAGCAUGAGAAAUUUUGCAAGAGAACUUGCUUUGUAUAGUAUUUAAGAACGCAAGAACAAAUGUUUUUGGCAUCUGCUUUUUUGCGCCCCUUUUGACAAAUCUAAAACGCCCUUGUCAAUCCUAGGAUUGGUUUAAGGACUGUUUACUAGGUUUAUCAAAUGGAGAUACUGCUCAAAGCAUCUAACUUAAAACAUUAAGUUUGGUUCUAUUGGUAAAUUUUCCAUGUACUAGCCUAACUUAAAAAGCUUAAAGAAACCUUAAAGGAAACUUUAAGCGAGGGAGAUUUUUUUAAGAAAGCUGUUAUCUAUUAACGCAUAGAAAGAAUUGAAGGAUUUUUACAAAAAAAUCACAGACAGGAGAAACAA ((((.(((.((((..........................((((((..(((((.(((((..(((((..((....(((((..........((((((........)))))).((((((...((((((...((((((((.....))......(((((((((((((((((...)))))))))))))))))......))))))))))))...(((((((((((((....((((.((((....(......((((((.(((((.....))))).))))))((((((((.((((((((...((((......).)))...))))))))))))))))....((((..........))))...)....)))).))))....)))))))))).)))..))))))........))))).(((.(((((........((((((.....(((((((((.((......)))))))).)))..(((((...(((((((((((((((((((....))))).......))))))))))))))..((((((((.(((.....(((((((((((((((....((..((((((.(((...))).))))))..))..))))))))))))).)).....))).))))))))..)))))((((((.....))))))((((.(((((....((.((((.(((((((....(((((.......))))).......))))))))))).))..)))))))))))))))..(((......((((((((.(((....))).))))))))....(((((......(((.(((((((((((................))))))))))).))).....(((((.((((.(((((...(((((((((((((..((((((((.....((((((((((.((((.....)))).))..))))))))..((.(((((.((((((((((((.(((((((((((....))))))..)))))..)))))..))))))).))))).))))))))))..)))))))...(((((((....))))))).))))))....))))).)))))))))..)))))...))).....)))))..)))..(((((((....))))))).))..)))))..))))).)...))))...(((((......))))).....))))))(((((((....))))))).)))))))...)))).. (-328.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 790 110 61 201 152 NC_009009:SSA_2318|5end_PilB-like_pili_biogenesis_ATPase,_putative_2321094..2321324_NEGATIVE 373 850 802 183 131 NC_009009:SSA_1243|5end_Dihydroorotate_dehydrogenase_electron_transfer_subunit,_putative_1268204..1268434_NEGATIVE 366 808 761 132 92 NC_009009:SSA_1312|5end_RADC-like_protein,_putative_1329663..1329893_NEGATIVE 364 428 383 88 43 NC_009009:SSA_0977|5end_3-isopropylmalate_dehydrogenase,_putative_982771..983001_POSITIVE 349 838 794 199 147 NC_009009:SSA_0238|5end_hypothetical_protein_232481..232711_POSITIVE 340 839 793 164 113 NC_009009:SSA_0825|5end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_803864..804094_POSITIVE 339 830 781 76 11 NC_009009:SSA_2056|5end_Cinnamoyl_ester_hydrolase,_putative_2058587..2058817_POSITIVE 337 838 791 204 146 NC_009009:SSA_0350|5end_Helicase,_putative_344218..344448_NEGATIVE 333 850 804 200 142 NC_009009:SSA_2047|5end_hypothetical_protein_2049953..2050183_NEGATIVE 333 840 792 74 30 NC_009009:SSA_0374|5end_Peptide_methionine_sulfoxide_reductase_msrA/msrB,_putative_363163..363393_POSITIVE 332 845 803 228 187 NC_009009:SSA_0990|5end_hypothetical_protein_991733..991963_POSITIVE 330 300 255 46 1 NC_009009:SSA_1234|5end_5'-nucleotidase,_putative_1259795..1260025_NEGATIVE 328 299 255 76 23 NC_009009:SSA_2121|5end_Cell_wall_surface_anchor_family_protein,_putative_2126907..2127137_NEGATIVE 327 826 782 74 12 NC_009009:SSA_1553|5end_Permease,_putative_1555047..1555277_POSITIVE 322 770 724 96 39 NC_009009:SSA_1447|5end_ATP_phosphoribosyltransferase,_putative_1449831..1450061_NEGATIVE 320 826 781 164 122 NC_009009:SSA_0940|5end_NOL1/NOP2/sun_family_protein,_putative_947626..947856_POSITIVE 320 845 803 191 148 NC_009009:SSA_0710|5end_Exopolysaccharide_biosynthesis_protein,_acetyltransferase,_putative_695639..695869_NEGATIVE 319 807 761 145 96 NC_009009:SSA_1683|5end_NrdI_protein,_putative_1677405..1677635_NEGATIVE 318 460 416 70 32 NC_009009:SSA_1629|5end_Peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type,_putative_1630338..1630568_POSITIVE 318 808 761 180 138 NC_009009:SSA_1203|5end_hypothetical_protein_1226985..1227215_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 366 808 761 80 40 NC_009009:SSA_1313|3end_hypothetical_protein_1329715..1329865_NEGATIVE 352 806 762 117 67 NC_009009:SSA_1278|3end_Rhodanese-like_domain_protein,_putative_1299563..1299713_NEGATIVE 337 838 791 144 86 NC_009009:SSA_0351|3end_Signal_peptidase_I,_putative_344278..344428_NEGATIVE 336 790 744 77 21 NC_009009:SSA_0531|3end_Ethanolamine_utilization_protein_eutQ_(cobalamin-dependent_degradation_of_ethanolamine),_putative_527884..528034_POSITIVE 331 750 707 112 54 NC_009009:SSA_0983|3end_Conserved_uncharacterized_protein_986945..987095_POSITIVE 327 410 361 65 20 NC_009009:SSA_2122|3end_hypothetical_protein_2127200..2127350_NEGATIVE 327 826 782 77 15 NC_009009:SSA_1552|3end_hypothetical_protein_1555130..1555280_POSITIVE 323 838 794 126 71 NC_009009:SSA_1869|3end_ATP-dependent_RNA_helicase,_putative_1864152..1864302_NEGATIVE 322 770 724 99 42 NC_009009:SSA_1448|3end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1449828..1449978_NEGATIVE 319 807 761 124 75 NC_009009:SSA_1684|3end_Histidine_kinase,_putative_1677426..1677576_NEGATIVE 309 819 771 130 80 NC_009009:SSA_0225|3end_10_kDa_chaperonin_219003..219153_POSITIVE 308 763 724 144 101 NC_009009:SSA_0116|3end_30S_ribosomal_protein_S17,_putative_112972..113122_POSITIVE 304 810 762 92 36 NC_009009:SSA_0333|3end_Mevalonate_kinase,_putative_327953..328103_POSITIVE 302 768 725 146 99 NC_009009:SSA_1905|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_1899276..1899426_NEGATIVE 302 837 797 75 32 NC_009009:SSA_0232|3end_hypothetical_protein_227277..227427_POSITIVE 301 819 780 151 105 NC_009009:SSA_2144|3end_Glutamyl-tRNA_synthetase,_putative_2144315..2144465_NEGATIVE 301 847 803 143 100 NC_009009:SSA_0952|3end_hypothetical_protein_958095..958245_POSITIVE 300 282 247 58 23 NC_009009:SSA_1038|3end_Lipoprotein,_putative_1053714..1053864_POSITIVE 298 757 716 57 9 NC_009009:SSA_1080|3end_Transcriptional_repressor_of_the_fructose_operon,_DeoR_family,_putative_1098361..1098511_POSITIVE 297 836 798 55 25 NC_009009:SSA_2049|3end_Polyribonucleotide_nucleotidyltransferase,_putative_2050693..2050843_NEGATIVE